Aims: To evaluate survival of pathogenic strains, Listeria monocytogenes and Salmonella Infantis and a sanitation indicator Enterococcus faecalis in composts at different stages of the composting process and during storage. Methods and Results: The studied pathogenic and indicator strains, originally isolated from compost, were inoculated into compost samples from the various stages of the composting process. During incubation, indigenous microflora diversity was monitored with DGGE analysis. After 90 days of incubation, strain survival was observed in compost sampled before the beginning of the cooling phase, and DGGE analysis demonstrated an increase of microbial diversity up to the cooling phase. However, inoculated strains were not detected in composts after 30, 60 or 90 days of incubation in compost sampled after the start of the cooling phase. Microbial diversity also became stable, and DGGE profiles reached a maximum number of bands at this stage. Conclusions: Strain survival was not observed in stabilized composts. The cooling phase seems to be the turning point for pathogen survival and at this stage the indigenous microflora appeared to play a significant role in suppression. Significance and Impact of the Study: The importance of indigenous microflora in the survival of pathogens in four different composts was demonstrated. Stabilized composts were recommended for spreading on land.